Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

ABSTRACT The genome sequences of intestinal Bacteroidales strains reveal evidence of extensive horizontal gene transfer. In vitro studies of Bacteroides and other bacteria have addressed mechanisms of conjugative transfer and some phenotypic outcomes of these DNA acquisitions in the recipient, such as the acquisition of antibiotic resistance. However, few studies have addressed the horizontal transfer of genetic elements between bacterial species coresident in natural microbial communities, especially microbial ecosystems of humans. Here, we examine the genomes of Bacteroidales species from two human adults to identify genetic elements that were likely transferred among these Bacteroidales while they were coresident in the intestine. Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity. These five regions are not found in any other sequenced Bacteroidetes genome at this level of identity and are likely all integrative conjugative elements (ICEs). Such highly similar and unique regions occur in only 0.4% of phylogenetically representative mock communities, providing strong evidence that these five regions were transferred between coresident strains in these subjects. In addition to the requisite proteins necessary for transfer, these elements encode proteins predicted to increase fitness, including orphan DNA methylases that may alter gene expression, fimbriae synthesis proteins that may facilitate attachment and the utilization of new substrates, putative secreted antimicrobial molecules, and a predicted type VI secretion system (T6SS), which may confer a competitive ecological advantage to these strains in their complex microbial ecosystem

Characterization of Adherent Bacteroidales from Intestinal Biopsies of Children and Young Adults with Inflammatory Bowel Disease

There is extensive evidence implicating the intestinal microbiota in inflammatory bowel disease [IBD], but no microbial agent has been identified as a sole causative agent. Bacteroidales are numerically dominant intestinal organisms that associate with the mucosal surface and have properties that both positively and negatively affect the host. To determine precise numbers and species of Bacteroidales adherent to the mucosal surface in IBD patients, we performed a comprehensive culture based analysis of intestinal biopsies from pediatric Crohn's disease [CD], ulcerative colitis [UC], and control subjects. We obtained biopsies from 94 patients and used multiplex PCR or 16S rDNA sequencing of Bacteroidales isolates for species identification. Eighteen different Bacteroidales species were identified in the study group, with up to ten different species per biopsy, a number higher than demonstrated using 16S rRNA gene sequencing methods. Species diversity was decreased in IBD compared to controls and with increasingly inflamed tissue. There were significant differences in predominant Bacteroidales species between biopsies from the three groups and from inflamed and uninflamed sites. Parabacteroides distasonis significantly decreased in inflamed tissue. All 373 Bacteroidales isolates collected in this study grew with mucin as the only utilizable carbon source suggesting this is a non-pathogenic feature of this bacterial order. Bacteroides fragilis isolates with the enterotoxin gene [bft], previously associated with flares of colitis, were not found more often at inflamed colonic sites or within IBD subjects. B. fragilis isolates with the ability to synthesize the immunomodulatory polysaccharide A [PSA], previously shown to be protective in murine models of colitis, were not detected more often from healthy versus inflamed tissue

Urbanization in French colonial Louisiana (1706-1766)

Zitomersky J. Urbanization in French colonial Louisiana (1706-1766). In: Annales de démographie historique, 1974. pp. 263-278

PSA analysis of <i>B. fragilis</i> isolates.

<p>A Western blot of PSA from <i>B. fragilis</i> isolates grown <i>in vitro</i> after isolation from control, CD and UC (inflamed (I) a non-inflamed (NI) biopsies. Panel A: Lanes 1–6 contain <i>B. fragilis</i> isolates from the biopsies control subjects (4, 6, 13, 34, 68, and 1). Lanes 7–8 contain isolates from non-inflamed and inflamed biopsies from subject 23 with UC. Lanes 9–11 contain isolates from inflamed and uninflamed biopsies from subjects with UC: 32, 29 and 77. Panel B: Lane 1 contains <i>B. fragilis</i> type strain 9343 as a positive control. Lanes 2 and 3 contain isolates from a non-inflamed and then an inflamed biopsy from subject 47 with CD. Lanes 4–8 contain <i>B. fragilis</i> isolates from inflamed biopsies of subjects 26, 56, 64, 14, and 85 with CD.</p

Total Bacteroidales [cfu/biopsy) and number of different Bacteroidales species detected per biopsy by diagnoses and degree of inflammation in entire cohort.

<p><i>P</i>-value from generalized estimating equation, controlling for within-subject correlation.</p

Total Bacteroidales (cfu/biopsy) by cohort and degree of inflammation.

<p>Biopsies were grouped by cohort: CD (Crohn Disease), UC (ulcerative colitis) and Control and degree of inflammation: no and mild inflammation (no/mild) or moderate to severe inflammation (mod/svr). N is equivalent to the number of biopsies in each group. Column level represents mean Bacteroidales log cfu/biopsy. Error bars represent inter-quartile ranges <b>A.</b> Entire cohort. There were no significant differences detected between cohorts. <b>B</b> Includes only biopsies from newly diagnosed subjects.</p

Number of biopsies with <i>B. fragilis</i> where <i>bft</i> or PSA was present.

<p>Abbreviations: CD =  Crohn Disease, UC =  Ulcerative Colitis, I =  Inflamed biopsy tissue, NI =  Non-Inflamed biopsy tissue where isolate originated.</p><p>Denominator represents all biopsies in a cohort where <i>B. fragilis</i> was detected and numerators indicate:</p><p>1. <i>bft</i> detected by PCR. (No statistically significant differences were detected between groups).</p><p>2. PSA1 detected by immunoblot. (No statistically significant differences were detected between groups).</p

Bacteroidales species diversity by degree of inflammation.

<p>The median number of species per IBD biopsy detected from biopsies with no or mild inflammation (No/Mild) compared to IBD biopsies with moderate to severe inflammation (Mod/Svr). Error bars represent inter-quartile ranges. N equals the number of biopsies in each group. *<i>P</i> = 0.02.</p

PCR analysis of <i>bft</i> from <i>B. fragilis</i> isolates.

<p>Lane one contains a <i>bft</i> containing strain (086 care of C. Sears, MD). Lane two contains a <i>B. fragilis</i> strain without <i>bft</i> (9343). Lane three contains an isolate from the terminal ileum (TI) of subject 34. Lanes four and five contain isolates from TI and ascending colon biopsies from control subject 43. Lane 6 contains an isolate from the non-inflamed terminal ileum of a subject 71 with CD. Lane 7 contains an isolate from an inflamed TI biopsy of subject 64 with CD. Lanes 8 and 9 contains isolates from non-inflamed rectal and inflamed ascending colon biopsies of a subject 74 with CD. Lanes 10 and 11 are isolates from non-inflamed TI and inflamed descending colon biopsies of a subject 39 with UC. Lanes 12 and 13 are isolates from an non-inflamed cecal biopsy and inflamed rectal biopsy from subject 62 with UC.</p